Evaluation of yield of currently available diagnostics by sample type to optimize detection of respiratory pathogens in patients with a community-acquired pneumonia

Respiratory virus concentrations in human excretions that contribute to wastewater: a systematic review and meta-analysis

Concentrations of nucleic acids from a range of respiratory viruses in wastewater solids collected from wastewater treatment plants correlate to clinical data on disease occurrence in the community contributing to the wastewater. Viral nucleic acids enter wastewater from excretions deposited in toilets or drains. To relate measured concentrations in wastewater at a treatment plant to the number of community infections, viral nucleic-acid concentrations in human excretions are needed as inputs to a mass balance model. Here, we carried out a systematic review and meta-analysis to characterize the concentrations and presence of influenza A and B, respiratory syncytial virus, metapneumovirus, parainfluenza virus, rhinovirus, and seasonal coronaviruses in stool, urine, mucus, sputum, and saliva. We identified 220 data sets from 50 articles and reported viral concentrations and presence in these excretions. Data were unevenly distributed across virus type (with the most available for influenza) and excretion type (with the most available for respiratory excretions). Most articles only reported the presence or absence of the virus in a cross-sectional study design. There is a need for more concentration data, including longitudinal data, across all respiratory virus and excretion types. Such data would allow quantitatively linking virus wastewater concentrations to numbers of infected individuals.

Adherence to use of blood cultures according to current national guidelines and their impact in patients with community acquired pneumonia: A retrospective cohort

BACKGROUND

Community acquired pneumonia (CAP) is the most frequent cause of mortality secondary to infectious etiologies. Recommendations about the use of blood cultures in the diagnosis and treatment of CAP has been a contentious topic of debate and ever-changing recommendations.

METHODS

A cohort study was conducted in a community teaching hospital. All the patients that were admitted with a diagnosis of CAP, between January and December of 2019 were included. Sociodemographic and clinical characteristics were obtained. Blood cultures results were obtained, and it was evaluated if they were done in compliance with current recommendations by the Infectious Disease Society of America (IDSA).

RESULTS

721 patients were included in the study. Median age was 68 years and 50% of the patients were male (n = 293). Patients presented from home (84%) and the most common comorbidities were hypertension and diabetes (68% and 31%). 96 patients had positive blood culture and 34% (n = 247) of all the blood cultures were adequately ordered. 80 patients died or went to hospice and the median length of hospital stay in our cohort was 7 days. The multivariate model showed that mortality was associated with positive blood cultures (OR = 3.1 95%CI 1.63-5.87) and appropriateness of blood cultures (OR = 2.96 95% CI 1.2-5.7).

CONCLUSION

Adequate use of blood cultures in patients with CAP might have some association with the outcomes of this disease. However, a prospective study evaluating the utility of this test following current IDSA recommendations is needed to understand their impact in mortality and morbidity.

Metagenomic next-generation sequencing identified psittacosis among poultry processing workers in Shandong Province, China

Human infection with Chlamydia psittaci is rare but difficult to recognize. We report an outbreak of psittacosis among poultry processing workers in China. We applied metagenomic next-generation sequencing and identified Chlamydia psittaci reads from samples of all seven patients, four of which were subsequently confirmed by PCR. Epidemiological results suggested that the poultry processed in the factory was the possible source of human infection.

Identified micro-organisms in hospitalized community-acquired pneumonia patients living near goat and poultry farms

BACKGROUND

In the Netherlands, an increased risk of community-acquired pneumonia (CAP) has been reported for adults living near goat and poultry farms. Previous results of respiratory microbiome studies in hospitalized CAP patients near poultry farms suggested a higher relative abundance of Streptococcus pneumoniae. This retrospective study, using routine laboratory data from hospitalized CAP patients, aims to explore possible aetiologic micro-organisms of CAP in relation to livestock exposure.

METHODS

Patient characteristics and PCR and urinary antigen test results were retrieved retrospectively from electronic medical records of CAP patients admitted to the Jeroen Bosch Hospital or Gelre Hospital in the Netherlands during 2016-2017. Distances between the patients' home address and the nearest poultry and goat farm were calculated. Differences in laboratory test results between CAP patients with and without goat or poultry farms within 2 km of their home address were analyzed using Fisher's exact test.

RESULTS

In total, 2230 CAP episodes with diagnostic results were included. In only 25% of the CAP episodes, a micro-organism was detected. A positive urinary antigen test for S. pneumoniae was found more often in patients living within two kilometers of goat (15.2% vs. 11.3%) and poultry farms (14.4% vs. 11.3%), however these differences were not statistically significant (p = 0.1047 and p = 0.1376).

CONCLUSION

Our retrospective analysis did not show statistically significant differences in the identified micro-organisms in hospitalized CAP patients related to livestock farming. The study was hampered by limited statistical power and limited laboratory results. Therefore, the potential increased CAP risk around goat and poultry farms will be further explored in a prospective study among CAP patients in primary care.

Evaluation of current practice of antimicrobial use and clinical outcome of patients with pneumonia at a tertiary care hospital in Ethiopia: A prospective observational study

BACKGROUND

Antimicrobial resistance, which is commonly observed in the management of pneumonia, is a major threat to public health and is driven by inappropriate antimicrobial use. The aim of this study was therefore to assess the current practice of antimicrobial utilization and clinical outcomes in the management of adult pneumonia at Tikur Anbessa Specialized Hospital.

METHOD

A prospective observational study was conducted in the internal medicine wards of Tikur Anbessa Specialized Hospital. The study was conducted from 1 September 2016 to 30 June 2017 and patients aged ≥ 14 years and diagnosed with pneumonia were included. Chart review and self-administered questionnaire were used to collect data regarding pneumonia diagnosis and management as well as clinical outcomes (stable, complications, and in-hospital mortality). Descriptive statistics and binary logistic regressions were performed for data analyses.

RESULTS

Out of 200 enrolled patients, clinical diagnosis was supported by microbiologic testing and imaging in 75 (37.5%) and 122 (61.0%) cases, respectively. The treatment approach in almost all patients (99.5%) was empirical and no de-escalation therapy was made even after acquiring culture results. The total duration of antimicrobial therapy was 12.05±5.09 days and vancomycin was the most commonly prescribed antimicrobial agent (25%), with 70% of the patients receiving this drug empirically. Nearly, 30% of the patients missed their antimicrobial doses during the course of treatment and stock-out (36.7%) was the major reason. Close to 113 (66%) of the treating physicians used reference books to prescribe antimicrobial agents. Patients' outcomes were found to be stable (66%), in-hospital mortality (18.5%), and ending up in complications (17%). Poor clinical outcome (death and complicated cases) was found to be associated with recent antimicrobial use history (p = 0.007, AOR 2.86(1.33-6.13)), cancer (p = 0.023, AOR 3.46(1.18-10.13)), recent recurrent upper respiratory tract infection (p = 0.046, AOR 3.70(1.02-13.40)), respiratory rate >24 breaths/min or <12 breaths/min (p = 0.013, AOR 2.45(1.21-4.95)) and high level of serum creatinine after initiation of antimicrobial therapy (>1.4mg/dl) (p = 0.032, AOR 2.37(1.07-5.20)).

CONCLUSION

Antimicrobials are empirically prescribed without sufficient evidence of indication and microbiological or radiological findings. The practice also is not based on local guidelines and no multidisciplinary approach is apparent. [How about: "It is likely that these factors contributed to higher rates of mortality (18.5%) when compared with similar studies in other countries" instead of this "As a result, there were higher rates of mortality (18.5%) when compared with other similar studies"]. Hence, the hospital requires a coordinated intervention to improve rational use of antimicrobials and clinical outcomes through establishing an antimicrobial stewardship program.

Time-course of upper respiratory tract viral infection and COPD exacerbation

Viral respiratory tract infections have been implicated as the predominant risk factor for acute exacerbations of chronic obstructive pulmonary disease (AECOPD). We aimed to evaluate, longitudinally, the association between upper respiratory tract infections (URTI) caused by viruses and AECOPD.Detection of 18 viruses was performed in naso- and orοpharyngeal swabs from 450 COPD patients (Global Initiative for Chronic Obstructive Lung Disease stages 2-4) who were followed for a mean of 27 months. Swabs were taken during stable periods (n=1909), at URTI onset (n=391), 10 days after the URTI (n=356) and during an AECOPD (n=177) and tested using a multiplex nucleic acid amplification test.Evidence of at least one respiratory virus was significantly higher at URTI onset (52.7%), 10 days after the URTI (15.2%) and during an AECOPD (38.4%), compared with the stable period (5.3%, p<0.001). During stable visits, rhinovirus accounted for 54.2% of all viral infections, followed by coronavirus (20.5%). None of the viruses were identified in two consecutive stable visits. Patients with a viral infection at URTI onset did not have a higher incidence of exacerbation than patients without viral infection (p=0.993). Τhe incidence of any viral infection during an AECOPD was similar between URTI-related AECOPD and non-URTI-related AECOPD (p=0.359). Only 24% of the patients that had a URTI-related AECOPD had the same virus at URTI onset and during an AECOPD. Detection of parainfluenza 3 at URTI onset was associated with a higher risk of an AECOPD (p=0.003). Rhinovirus and coronavirus were the most frequently detected viruses during AECOPD visits, accounting for 35.7% and 25.9% of all viral infections, respectively.The prevalence of viral infection during the stable period of COPD was low. The risk of exacerbation following the onset of URTI symptoms depends on the particular virus associated with the event and was significant only for parainfluenza 3.

Episodic viral wheeze and multiple-trigger wheeze in preschool children are neither distinct nor constant patterns. A prospective multicenter cohort study in secondary care

OBJECTIVES

To evaluate whether episodic viral wheeze (EVW) and multiple-trigger wheeze (MTW) are clinically distinguishable and stable preschool wheezing phenotypes.

METHODS

Children of age 1 to 4 year with recurrent, pediatrician-confirmed wheeze were recruited from secondary care; 189 were included. Respiratory and viral upper respiratory tract infection (URTI) symptoms were recorded weekly by parents in an electronic diary during 12 months. Every 3 months, diary-based symptoms were classified as EVW or MTW and compared to phenotypes assigned by pediatricians based on clinical history. We collected nasal samples for respiratory virus PCR during URTI, respiratory symptoms and in absence of symptoms.

RESULTS

Of 660 3-month periods, the diary-based phenotype was EVW in 11%, MTW in 54% and 35% were free from respiratory episodes. Pediatrician-based classification showed 59% EVW and 26% MTW. The Kappa measure of agreement between diary-based and pediatrician-assigned phenotypes was very low (0.12, 95%CI, 0.07-0.17). Phenotypic instability was observed in 32% of cases. PCR was positive in 71% during URTI symptoms, 66% during respiratory symptoms and 38% in the absence of symptoms.

CONCLUSION

This study shows that EVW and MTW are variable over time within patients. Pediatrician classification of these phenotypes based on clinical history does not correspond to prospectively recorded symptom patterns. The applicability of these phenotypes as a basis for therapeutic decisions and prognosis should be questioned.

Comparing the yield of oropharyngeal swabs and sputum for detection of 11 common pathogens in hospitalized children with lower respiratory tract infection

Background

Advances in molecular laboratory techniques are changing the prospects for the diagnosis of viral infectious diseases. Multiplex polymerase chain reaction assay (multiplex-PCR) can detect dozens of pathogens simultaneously, greatly reducing turnaround time (TAT) and improving detection sensitivity. But as a double-edged sword, due to the high sensitivity of PCR, the type of respiratory specimens is critical to diagnosis. In this work, we performed a head-to-head comparison to evaluate the multiplex-PCR yields between two samples, sputum and flocked oropharyngeal swabs (OPS).

Methods

Eleven common respiratory pathogens were tested in hospitalized children< 13 years of age who met the criteria for lower respiratory tract infection by GeXP-based multiplex-PCR of paired OPS and sputum.

Results

From January to June 2018, 440 children with paired OPS and sputum were tested. The positive rate was 84% (369/440) for OPS and 88% (386/440) for sputum (p = .007). The frequency of detection of HRV, RSV, Influenza A virus, HMPV, parainfluenza virus, adenovirus, M. pneumoniae, coronavirus, bocavirus and C. pneumoniae in sputa was higher than that of OPSs (all p < .001). Both types of specimens had similarly very good kappa values for most of pathogens, except for Mycoplasma pneumonia (κ = 0.61) and Chlamydia pneumoniae (κ = 0.24). Additionally, 79.3% (349/440) of cases showed consistent results between the two types of samples, and they were significantly younger than patients with inconsistent results (p = .002).

Conclusions

Flocked oropharyngeal swabs and sputum performed similarly for the detection of common respiratory pathogens in hospitalized children by multiplex-PCR, except for Mycoplasma pneumoniae and Chlamydia pneumoniae. Young patients are likely to have consistent results between the two specimens.

Electronic supplementary material

The online version of this article (10.1186/s12985-019-1177-x) contains supplementary material, which is available to authorized users.

A Haemophilus sp. dominates the microbiota of sputum from UK adults with non-severe community acquired pneumonia and chronic lung disease

The demographics and comorbidities of patients with community acquired pneumonia (CAP) vary enormously but stratified treatment is difficult because aetiological studies have failed to comprehensively identify the pathogens. Our aim was to describe the bacterial microbiota of CAP and relate these to clinical characteristics in order to inform future trials of treatment stratified by co-morbidity. CAP patients were prospectively recruited at two UK hospitals. We used 16S rRNA gene sequencing to identify the dominant bacteria in sputum and compositional data analysis to determine associations with patient characteristics. We analysed sputum samples from 77 patients and found a Streptococcus sp. and a Haemophilus sp. were the most relatively abundant pathogens. The Haemophilus sp. was more likely to be dominant in patients with pre-existing lung disease, and its relative abundance was associated with qPCR levels of Haemophilus influenzae. The most abundant Streptococcus sp. was associated with qPCR levels of Streptococcus pneumoniae but dominance could not be predicted from clinical characteristics. These data suggest chronic lung disease influences the microbiota of sputum in patients with CAP. This finding could inform a trial of stratifying empirical CAP antibiotics to target Haemophilus spp. in addition to Streptococcus spp. in those with chronic lung disease.

Laboratory methods for case finding in human psittacosis outbreaks: a systematic review

Background

Psittacosis outbreak investigations require rapid identification of cases in order to trace possible sources and perform public health risk assessments. In recent outbreaks in the Netherlands, such investigations were hampered by the non-specificity of laboratory testing methods to identify human Chlamydia psittaci infections.

Method

A systematic search of PubMed and Scopus databases of literature published between 01 January, 1986 and 03 July, 2017 was done to find best practices of laboratory-testing methods used in psittacosis outbreaks of two or more human cases. Reference lists of included articles were hand searched to identify additional articles.

Results

Thirty-seven eligible articles were identified, describing 44 human psittacosis outbreaks in 12 countries. Laboratory tests performed were PCR (with various targets), serologic tests (complement binding reactions, ELISA’s, immunofluorescence tests and immuno-peroxidase tests) and culture, in various combinations. The literature provided no ‘gold standard’ laboratory testing strategy to identify recent human C. psittaci infections. In most psittacosis outbreaks, for a considerable number of cases (or tested individuals in an exposed cohort), C. psittaci infection could not be confirmed, nor excluded as causative pathogen. None of the testing strategies was found to be suitable for (nearly) full case finding.

Conclusion

PCR enables rapid identification of human psittacosis patients and helps source finding by genotyping but has the disadvantage that sensitivity is high only in the acute phase. In outbreak situations, there is often a time delay and therefore, there is a need for new serologic testing methods next to PCR, with good specificity and sensitivity. Moreover, serum is easier to collect than the preferred diagnostic materials for PCR. A serologic test that can reliably confirm infection status without the necessity of convalescent serum sampling would enhance case finding, source tracing, identification of risk factors and assessment of burden of disease in various settings.

Electronic supplementary material

The online version of this article (10.1186/s12879-018-3317-0) contains supplementary material, which is available to authorized users.

Prevalence of Carbapenem-Resistant Gram-Negative Infections in the United States Predominated by Acinetobacter baumannii and Pseudomonas aeruginosa

Background

Carbapenem-resistant (CR) Gram-negative pathogens are recognized as a major health concern. This study examined the prevalence of infections due to 4 CR Gram-negative species (Acinetobacter baumannii, Pseudomonas aeruginosa, Klebsiella pneumoniae, and Escherichia coli) in the United States and assessed their impact on hospital stays and mortality.

Methods

Hospitalized patients with laboratory-confirmed infection due to any of the 4 Gram-negative pathogens were identified from the Premier Healthcare Database. Proportions of CR were calculated by pathogen and infection site (blood, respiratory, urinary, or other) for the United States as whole and by census regions. Crude and adjusted odds ratios for in-hospital mortality were produced using logistic regression.

Results

From 2009 to 2013, 13 262 (4.5%) of 292 742 infections due to these 4 Gram-negative pathogens were CR. Of these CR infections, 82.3% were caused by A. baumannii (22%) or P. aeruginosa (60.3%), while 17.7% were caused by K. pneumoniae or E. coli. CR patients had longer hospital stays than carbapenem-susceptible (CS) patients in all pathogen-infection site cohorts, except in the A. baumannii-respiratory cohort. The crude all cause in-hospital mortality was greater for most pathogen-infection site cohorts of the CR group compared with the CS group, especially for A. baumannii infection in the blood (crude odds ratio [OR], 3.91; 95% confidence interval [CI], 2.69–5.70). This difference for the A. baumannii-blood cohort remained after adjusting for the relevant covariates (adjusted OR, 2.46; 95% CI, 1.43–4.22).

Conclusion

The majority of CR infections and disease burden in the United States was caused by nonfermenters A. baumannii and P. aeruginosa. Patients with CR infections had longer hospital stays and higher crude in-hospital mortality.

Clinical Application of High-Resolution Computed Tomographic Imaging Features of Community-Acquired Pneumonia

Background

This article discusses the value of high-resolution computed tomography (HRCT) in the diagnosis and treatment of pulmonary infections. Lung infection caused by pathogens is an important cause of death. Traditional methods to treat lung infection involved empirical antibiotic therapy. Thin-slice CT scanning is widely used in the clinical setting, and HRCT scan can very clearly show alveolar and bronchiolar involvement of infection.

Material/Methods

In total, 178 patients with community-acquired pneumonia (CAP) were enrolled. All the patients underwent CT scan, qualified sputum, and blood samples for culture or immunological biochemical tests. CT imaging features, pathogenic bacteria, and treatment results were used for statistical analysis.

Results

In 77 patients with lobar consolidation, the rate of detection was 43.26% (77/178), and in 101 patients with lobular pneumonia it was 56.74% (101/178). In 51 patients, pathogenic bacteria were detected (28.65%, 51/178). Sixteen of 33 patients detected with bacteria had cavities (48.5%, 16/33) and 35 of 145 patients detected with bacteria had no cavities (24.1%, 35/145). The difference between the 2 groups was statistically significant (χ²=7.795, P=0.005). According to the pathogenic bacteria, 38 patients were cured (74.51%, 38/51), and according to the CT imaging features 81 patients were cured (71.05%, 81/114). No statistically significant difference was found between them (χ²=0.209, P=0.647).

Conclusions

Treatment effect of CAP based on HRCT findings is not inferior to treatment effect guided by microbial characterization.

Comparison of Luminex xTAG® RVP fast assay and real time RT-PCR for the detection of respiratory viruses in adults with community-acquired pneumonia

Community‐acquired pneumonia (CAP) is the third cause of death worldwide. Viruses are frequently detected in adult CAP. Highly sensitive diagnostic techniques should be used due to poor viral shedding. Different sampling methods can affect viral detection, being necessary to establish the optimal type of sample for identifying respiratory viruses in adults. The detection rates of respiratory viruses by Luminex xTAG® RVP fast assay, real time RT‐PCR (rtRT‐PCR) (Sacace®), and immunofluorescence assay (IFA) in adult CAP were performed in nasopharyngeal swabs (NPS) and aspirates (NPA) from 179 hospitalized adults. Positivity was 47.5% for Luminex®, 42.5% for rtRT‐PCR (P = 0.3), and 2.7% for IFA (2.7%) (P < 0.0). The sensitivity, specificity, and kappa coefficient of xTAG® RVP compared with rtRT‐PCR were 84.2%, 79.6%, and 0.62%, respectively. Luminex® and rtRT‐PCR detected 65 (58.0%) and 57 (50.9%) viruses in 112 NPA and 35 (34.3%) and 31 (30.4%) in 102 NPS, respectively (P < 0.01). xTAG® RVP is appropriate for detecting respiratory viruses in CAP adults. Both molecular techniques yielded better results with nasopharyngeal aspirate than swabs. J. Med. Virol. 88:1173–1179, 2016. © 2016 Wiley Periodicals, Inc.

Development of two real-time multiplex PCR assays for the detection and quantification of eight key bacterial pathogens in lower respiratory tract infections

The frequent lack of a positive and timely microbiological diagnosis in patients with lower respiratory tract infection (LRTI) is an important obstacle to antimicrobial stewardship. Patients are typically prescribed broad-spectrum empirical antibiotics while microbiology results are awaited, but, because these are often slow, negative, or inconclusive, de-escalation to narrow-spectrum agents rarely occurs in clinical practice. The aim of this study was to develop and evaluate two multiplex real-time PCR assays for the sensitive detection and accurate quantification of Streptococcus pneumoniae, Haemophilus influenzae, Staphylococcus aureus, Moraxella catarrhalis, Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Acinetobacter baumannii. We found that all eight bacterial targets could be reliably quantified from sputum specimens down to a concentration of 100 CFUs/reaction (8333 CFUs/mL). Furthermore, all 249 positive control isolates were correctly detected with our assay, demonstrating effectiveness on both reference strains and local clinical isolates. The specificity was 98% on a panel of nearly 100 negative control isolates. Bacterial load was quantified accurately when three bacterial targets were present in mixtures of varying concentrations, mimicking likely clinical scenarios in LRTI. Concordance with culture was 100% for culture-positive sputum specimens, and 90% for bronchoalveolar lavage fluid specimens, and additional culture-negative bacterial infections were detected and quantified. In conclusion, a quantitative molecular test for eight key bacterial causes of LRTI has the potential to provide a more sensitive decision-making tool, closer to the time-point of patient admission than current standard methods. This should facilitate de-escalation from broad-spectrum to narrow-spectrum antibiotics, substantially improving patient management and supporting efforts to curtail inappropriate antibiotic use.